We use the Open Graph Benchmarks Large-Scale Challenge (OGB-LSC) [1]} for our exploration on the importance of 3D structure for molecular properties. The PubChem Quantum Mechanics for Molecules (PCQM4M), a part of the OGB-LSC, is a quantum chemistry dataset with about 4 million molecular samples created by the PubChemQC project [2]}, [3]}. This is a subset of the larger PubChem database, which hosts more than 60 million chemical structures [4]}.
The training subset of the OGB-LSC-PCQM4Mv2 dataset, with 3.3 million molecules, contains 3D coordinate information derived from DFT. Each molecule sample are of varying sizes and a wide array of elements. The dataset sample includes the 3D structures of the molecule and it's accompanying HOMO-LUMO energy gap calculated using DFT. We use 3D coordinates to generate the grids for our model.
